## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.68)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                          ORF4 1.0000000 1.0000000 1.0000000
##  3:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  4:       1                          ORF9 1.0000000 1.0000000 1.0000000
##  5:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF18 1.0000000 1.0000000 1.0000000
##  8:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF30 1.0000000 1.0000000 1.0000000
## 10:       1                         ORF31 1.0000000 1.0000000 1.0000000
## 11:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 12:       1                         ORF38 1.0000000 1.0000000 1.0000000
## 13:       1    ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 14:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 15:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 16:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 17:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 18:       1                  ORF69, ORF70 1.0000000 1.0000000 1.0000000
## 19:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 20:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 21:       2                          ORF2 0.7048446 0.8666192 0.8075293
## 22:       2                          ORF3 0.7048446 0.8666192 0.8075293
## 23:       2                          ORF8 0.7048446 0.8666192 0.8075293
## 24:       2           ORF12, ORF13, ORF14 0.7048446 0.8666192 0.8075293
## 25:       2                         ORF22 0.7048446 0.8666192 0.8075293
## 26:       2                         ORF23 0.7048446 0.8666192 0.8075293
## 27:       2                         ORF24 0.7048446 0.8666192 0.8075293
## 28:       2           ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 29:       2                  ORF28, ORF29 0.7048446 0.8666192 0.8075293
## 30:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 31:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 32:       2                         ORF37 0.7048446 0.8666192 0.8075293
## 33:       2                         ORF39 0.7048446 0.8666192 0.8075293
## 34:       2                           CTO 0.7048446 0.8666192 0.8075293
## 35:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 36:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 37:       2                         ORF44 0.7048446 0.8666192 0.8075293
## 38:       2                  ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 39:       2     ORF62, ORF61, ORF60,ORF59 0.7048446 0.8666192 0.8075293
## 40:       2                       ORF66_1 0.7048446 0.8666192 0.8075293
## 41:       3    ORF18, ORF17, ORF16, ORF15 0.9968786 0.9990302 0.9826369
## 42:       3                         ORF19 0.9968786 0.9990302 0.9826369
## 43:       3                         ORF52 0.9968786 0.9990302 0.9826369
## 44:       3                  ORF57, ORF58 0.9968786 0.9990302 0.9826369
## 45:       3           ORF71, ORF72, ORF73 0.9968786 0.9990302 0.9826369
## 46:       4                  ORF53, ORF54 0.2153731 0.6088215 0.6060342
## 47:       5                       ORF64_1 0.2097334 0.6269125 0.5728833
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 16: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 17: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 18: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 19: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 20: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 28: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 29: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 30: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 31: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 32: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 33: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 34: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 35: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 36: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 37: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 38: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 39: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 40: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 41: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 42: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 43: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 44: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 45: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 46: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 47: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF69, ORF70"                 "ORF37, ORF36, ORF35, ORF35.5"
## [1] 2
##  [1] "ORF2"                         "ORF3"                        
##  [3] "ORF8"                         "ORF12, ORF13, ORF14"         
##  [5] "ORF22"                        "ORF23"                       
##  [7] "ORF24"                        "ORF27, ORF26, ORF25"         
##  [9] "ORF28, ORF29"                 "ORF37, ORF36, ORF35, ORF35.5"
## [11] "ORF36"                        "ORF37"                       
## [13] "ORF39"                        "CTO"                         
## [15] "ORF40"                        "ORF41, ORF42, OF43"          
## [17] "ORF44"                        "ORF45, ORF46"                
## [19] "ORF62, ORF61, ORF60,ORF59"    "ORF66_1"                     
## [21] "ORF53, ORF54"                 "ORF64_1"
## [1] 22

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                          ORF9 1.0000000 1.0000000 1.0000000
##  4:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  5:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF18 1.0000000 1.0000000 1.0000000
##  7:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  8:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  9:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 10:       1                         ORF38 1.0000000 1.0000000 1.0000000
## 11:       1    ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 12:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 13:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 14:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 15:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 16:       2                          ORF2 0.7048446 0.8666192 0.8075293
## 17:       2                          ORF3 0.7048446 0.8666192 0.8075293
## 18:       2                          ORF8 0.7048446 0.8666192 0.8075293
## 19:       2           ORF12, ORF13, ORF14 0.7048446 0.8666192 0.8075293
## 20:       2                         ORF22 0.7048446 0.8666192 0.8075293
## 21:       2                         ORF23 0.7048446 0.8666192 0.8075293
## 22:       2                         ORF24 0.7048446 0.8666192 0.8075293
## 23:       2           ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 24:       2                  ORF28, ORF29 0.7048446 0.8666192 0.8075293
## 25:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 26:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 27:       2                         ORF37 0.7048446 0.8666192 0.8075293
## 28:       2                         ORF39 0.7048446 0.8666192 0.8075293
## 29:       2                           CTO 0.7048446 0.8666192 0.8075293
## 30:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 31:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 32:       2                         ORF44 0.7048446 0.8666192 0.8075293
## 33:       2                  ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 34:       2     ORF62, ORF61, ORF60,ORF59 0.7048446 0.8666192 0.8075293
## 35:       2                       ORF66_1 0.7048446 0.8666192 0.8075293
## 36:       3                          ORF4 0.9968786 0.9990302 0.9826369
## 37:       3                         ORF31 0.9968786 0.9990302 0.9826369
## 38:       3                       ORF65_1 0.9968786 0.9990302 0.9826369
## 39:       3                ORF68, ORF67_1 0.9968786 0.9990302 0.9826369
## 40:       3                  ORF69, ORF70 0.9968786 0.9990302 0.9826369
## 41:       4    ORF18, ORF17, ORF16, ORF15 0.2153731 0.6088215 0.6060342
## 42:       4                         ORF19 0.2153731 0.6088215 0.6060342
## 43:       4                         ORF52 0.2153731 0.6088215 0.6060342
## 44:       4                  ORF57, ORF58 0.2153731 0.6088215 0.6060342
## 45:       4           ORF71, ORF72, ORF73 0.2153731 0.6088215 0.6060342
## 46:       5                  ORF53, ORF54 0.2097334 0.6269125 0.5728833
## 47:       6                       ORF64_1 0.9902010 0.9978135 0.9076866
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 16: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 17: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 18: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 19: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 20: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 28: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 29: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 30: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 31: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 32: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 33: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 34: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 35: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 36: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 37: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 38: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 39: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 40: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 41: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 42: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 43: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 44: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 45: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 46: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 47: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF74, ORF75, ORF76, ORF67 _2" "ORF37, ORF36, ORF35, ORF35.5"
## [1] 2
##  [1] "ORF2"                         "ORF3"                        
##  [3] "ORF8"                         "ORF12, ORF13, ORF14"         
##  [5] "ORF22"                        "ORF23"                       
##  [7] "ORF24"                        "ORF27, ORF26, ORF25"         
##  [9] "ORF28, ORF29"                 "ORF37, ORF36, ORF35, ORF35.5"
## [11] "ORF36"                        "ORF37"                       
## [13] "ORF39"                        "CTO"                         
## [15] "ORF40"                        "ORF41, ORF42, OF43"          
## [17] "ORF44"                        "ORF45, ORF46"                
## [19] "ORF62, ORF61, ORF60,ORF59"    "ORF66_1"                     
## [21] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [23] "ORF52"                        "ORF57, ORF58"                
## [25] "ORF71, ORF72, ORF73"          "ORF53, ORF54"
## [1] 26

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                          ORF9 1.0000000 1.0000000 1.0000000
##  4:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  5:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF18 1.0000000 1.0000000 1.0000000
##  7:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  8:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  9:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 10:       1                         ORF38 1.0000000 1.0000000 1.0000000
## 11:       1    ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 12:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 13:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 14:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 15:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 16:       2                          ORF2 0.7048446 0.8666192 0.8075293
## 17:       2                          ORF8 0.7048446 0.8666192 0.8075293
## 18:       2                         ORF23 0.7048446 0.8666192 0.8075293
## 19:       2                         ORF24 0.7048446 0.8666192 0.8075293
## 20:       2           ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 21:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 22:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 23:       2                         ORF39 0.7048446 0.8666192 0.8075293
## 24:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 25:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 26:       2                  ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 27:       3                          ORF3 0.9968786 0.9990302 0.9826369
## 28:       3           ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 29:       3                         ORF22 0.9968786 0.9990302 0.9826369
## 30:       3                  ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 31:       3                         ORF37 0.9968786 0.9990302 0.9826369
## 32:       3                           CTO 0.9968786 0.9990302 0.9826369
## 33:       3                         ORF44 0.9968786 0.9990302 0.9826369
## 34:       3     ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 35:       3                       ORF66_1 0.9968786 0.9990302 0.9826369
## 36:       4                          ORF4 0.2153731 0.6088215 0.6060342
## 37:       4                         ORF31 0.2153731 0.6088215 0.6060342
## 38:       4                       ORF65_1 0.2153731 0.6088215 0.6060342
## 39:       4                ORF68, ORF67_1 0.2153731 0.6088215 0.6060342
## 40:       4                  ORF69, ORF70 0.2153731 0.6088215 0.6060342
## 41:       5    ORF18, ORF17, ORF16, ORF15 0.2097334 0.6269125 0.5728833
## 42:       5                         ORF19 0.2097334 0.6269125 0.5728833
## 43:       5                         ORF52 0.2097334 0.6269125 0.5728833
## 44:       5                  ORF57, ORF58 0.2097334 0.6269125 0.5728833
## 45:       5           ORF71, ORF72, ORF73 0.2097334 0.6269125 0.5728833
## 46:       6                  ORF53, ORF54 0.9902010 0.9978135 0.9076866
## 47:       7                       ORF64_1 0.6046887 0.8596618 0.6312348
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
## 16: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 17: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 18: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 19: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 20: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 28: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 29: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 30: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 31: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 32: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 33: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 34: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 35: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 36: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 37: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 38: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 39: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 40: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 41: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 42: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 43: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 44: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 45: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 46: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 47: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF74, ORF75, ORF76, ORF67 _2"
## [1] 1
##  [1] "ORF2"                         "ORF8"                        
##  [3] "ORF23"                        "ORF24"                       
##  [5] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
##  [7] "ORF36"                        "ORF39"                       
##  [9] "ORF40"                        "ORF41, ORF42, OF43"          
## [11] "ORF45, ORF46"                 "ORF4"                        
## [13] "ORF31"                        "ORF65_1"                     
## [15] "ORF68, ORF67_1"               "ORF69, ORF70"                
## [17] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [19] "ORF52"                        "ORF57, ORF58"                
## [21] "ORF71, ORF72, ORF73"          "ORF64_1"
## [1] 22

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  5:       1                         ORF63 1.0000000 1.0000000 1.0000000
##  6:       2                          ORF2 0.7048446 0.8666192 0.8075293
##  7:       2                          ORF8 0.7048446 0.8666192 0.8075293
##  8:       2                         ORF23 0.7048446 0.8666192 0.8075293
##  9:       2                         ORF24 0.7048446 0.8666192 0.8075293
## 10:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 11:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 12:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 13:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 14:       3                          ORF3 0.9968786 0.9990302 0.9826369
## 15:       3           ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 16:       3                         ORF22 0.9968786 0.9990302 0.9826369
## 17:       3                  ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 18:       3                         ORF37 0.9968786 0.9990302 0.9826369
## 19:       3                           CTO 0.9968786 0.9990302 0.9826369
## 20:       3                         ORF44 0.9968786 0.9990302 0.9826369
## 21:       3     ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 22:       3                       ORF66_1 0.9968786 0.9990302 0.9826369
## 23:       4                          ORF4 0.2153731 0.6088215 0.6060342
## 24:       4                         ORF31 0.2153731 0.6088215 0.6060342
## 25:       4                       ORF65_1 0.2153731 0.6088215 0.6060342
## 26:       4                ORF68, ORF67_1 0.2153731 0.6088215 0.6060342
## 27:       4                  ORF69, ORF70 0.2153731 0.6088215 0.6060342
## 28:       5                          ORF9 0.2097334 0.6269125 0.5728833
## 29:       5                  ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 30:       5                         ORF18 0.2097334 0.6269125 0.5728833
## 31:       5           ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 32:       5           ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 33:       5                         ORF38 0.2097334 0.6269125 0.5728833
## 34:       5    ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 35:       5                        NOIR_1 0.2097334 0.6269125 0.5728833
## 36:       5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 37:       5                        NOIR_2 0.2097334 0.6269125 0.5728833
## 38:       6    ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 39:       7                         ORF19 0.6046887 0.8596618 0.6312348
## 40:       7                         ORF52 0.6046887 0.8596618 0.6312348
## 41:       7                  ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 42:       7           ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 43:       8           ORF27, ORF26, ORF25 0.9713771 0.9899227 0.9410908
## 44:       8                         ORF39 0.9713771 0.9899227 0.9410908
## 45:       8                  ORF45, ORF46 0.9713771 0.9899227 0.9410908
## 46:       9                  ORF53, ORF54 0.9581874 0.9844445 0.9335398
## 47:      10                       ORF64_1 0.7865513 0.9466014 0.6044383
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 25: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 26: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 27: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 35: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 36: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 37: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 38: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 39: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 40: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 41: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 42: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 43: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 44: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 45: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 46: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 47: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF74, ORF75, ORF76, ORF67 _2"
## [1] 1
##  [1] "ORF2"                          "ORF8"                         
##  [3] "ORF23"                         "ORF24"                        
##  [5] "ORF37, ORF36, ORF35, ORF35.5"  "ORF36"                        
##  [7] "ORF40"                         "ORF41, ORF42, OF43"           
##  [9] "ORF4"                          "ORF31"                        
## [11] "ORF65_1"                       "ORF68, ORF67_1"               
## [13] "ORF69, ORF70"                  "ORF9"                         
## [15] "ORF10, ORF11"                  "ORF18"                        
## [17] "ORF22, ORF21, ORF20"           "ORF32, ORF33, ORF34"          
## [19] "ORF38"                         "ORF48, ORF49, ORF50, ORF51"   
## [21] "NOIR_1"                        "ORF74, ORF75, ORF76, ORF67 _2"
## [23] "NOIR_2"                        "ORF19"                        
## [25] "ORF52"                         "ORF57, ORF58"                 
## [27] "ORF71, ORF72, ORF73"           "ORF64_1"
## [1] 28

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  5:       1                         ORF63 1.0000000 1.0000000 1.0000000
##  6:       2                          ORF2 0.7048446 0.8666192 0.8075293
##  7:       2                          ORF8 0.7048446 0.8666192 0.8075293
##  8:       2                         ORF23 0.7048446 0.8666192 0.8075293
##  9:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 10:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 11:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 12:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 13:       3                          ORF3 0.9968786 0.9990302 0.9826369
## 14:       3           ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 15:       3                         ORF22 0.9968786 0.9990302 0.9826369
## 16:       3                  ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 17:       3                         ORF37 0.9968786 0.9990302 0.9826369
## 18:       3                           CTO 0.9968786 0.9990302 0.9826369
## 19:       3                         ORF44 0.9968786 0.9990302 0.9826369
## 20:       3     ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 21:       3                       ORF66_1 0.9968786 0.9990302 0.9826369
## 22:       4                          ORF4 0.2153731 0.6088215 0.6060342
## 23:       4                         ORF31 0.2153731 0.6088215 0.6060342
## 24:       5                          ORF9 0.2097334 0.6269125 0.5728833
## 25:       5                  ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 26:       5                         ORF18 0.2097334 0.6269125 0.5728833
## 27:       5           ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 28:       5           ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 29:       5                         ORF38 0.2097334 0.6269125 0.5728833
## 30:       5    ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 31:       5                        NOIR_1 0.2097334 0.6269125 0.5728833
## 32:       5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 33:       5                        NOIR_2 0.2097334 0.6269125 0.5728833
## 34:       6    ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 35:       7                         ORF19 0.6046887 0.8596618 0.6312348
## 36:       7                         ORF52 0.6046887 0.8596618 0.6312348
## 37:       7                  ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 38:       7           ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 39:       8                         ORF24 0.9713771 0.9899227 0.9410908
## 40:       9           ORF27, ORF26, ORF25 0.9581874 0.9844445 0.9335398
## 41:       9                         ORF39 0.9581874 0.9844445 0.9335398
## 42:       9                  ORF45, ORF46 0.9581874 0.9844445 0.9335398
## 43:      10                  ORF53, ORF54 0.7865513 0.9466014 0.6044383
## 44:      11                       ORF64_1 0.9397368 0.9807196 0.8714120
## 45:      12                       ORF65_1 0.4822671 0.8939242 0.3442378
## 46:      12                ORF68, ORF67_1 0.4822671 0.8939242 0.3442378
## 47:      12                  ORF69, ORF70 0.4822671 0.8939242 0.3442378
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 25: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 26: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 27: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 35: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 36: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 37: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 38: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 39: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 40: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 41: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 42: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 43: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
## 44: 0.010922854 0.0043986223 0.003738478 -1.6009673 0.467876036 0.71047807
## 45: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 46: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 47: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF3"                          "ORF74, ORF75, ORF76, ORF67 _2"
## [1] 2
##  [1] "ORF2"                          "ORF8"                         
##  [3] "ORF23"                         "ORF37, ORF36, ORF35, ORF35.5" 
##  [5] "ORF36"                         "ORF40"                        
##  [7] "ORF41, ORF42, OF43"            "ORF4"                         
##  [9] "ORF31"                         "ORF9"                         
## [11] "ORF10, ORF11"                  "ORF18"                        
## [13] "ORF22, ORF21, ORF20"           "ORF32, ORF33, ORF34"          
## [15] "ORF38"                         "ORF48, ORF49, ORF50, ORF51"   
## [17] "NOIR_1"                        "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2"                        "ORF19"                        
## [21] "ORF52"                         "ORF57, ORF58"                 
## [23] "ORF71, ORF72, ORF73"           "ORF53, ORF54"                 
## [25] "ORF65_1"                       "ORF68, ORF67_1"               
## [27] "ORF69, ORF70"
## [1] 27

Selected number of clusters: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  5:       1                         ORF63 1.0000000 1.0000000 1.0000000
##  6:       2                          ORF2 0.7048446 0.8666192 0.8075293
##  7:       2                          ORF8 0.7048446 0.8666192 0.8075293
##  8:       2                         ORF23 0.7048446 0.8666192 0.8075293
##  9:       2  ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 10:       2                         ORF36 0.7048446 0.8666192 0.8075293
## 11:       2                         ORF40 0.7048446 0.8666192 0.8075293
## 12:       2            ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 13:       3                          ORF3 0.9968786 0.9990302 0.9826369
## 14:       3           ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 15:       3                         ORF22 0.9968786 0.9990302 0.9826369
## 16:       3                  ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 17:       3                         ORF37 0.9968786 0.9990302 0.9826369
## 18:       3                           CTO 0.9968786 0.9990302 0.9826369
## 19:       3                         ORF44 0.9968786 0.9990302 0.9826369
## 20:       3     ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 21:       3                       ORF66_1 0.9968786 0.9990302 0.9826369
## 22:       4                          ORF4 0.2153731 0.6088215 0.6060342
## 23:       4                         ORF31 0.2153731 0.6088215 0.6060342
## 24:       5                          ORF9 0.2097334 0.6269125 0.5728833
## 25:       5                  ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 26:       5                         ORF18 0.2097334 0.6269125 0.5728833
## 27:       5           ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 28:       5           ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 29:       5                         ORF38 0.2097334 0.6269125 0.5728833
## 30:       5    ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 31:       5                        NOIR_1 0.2097334 0.6269125 0.5728833
## 32:       5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 33:       5                        NOIR_2 0.2097334 0.6269125 0.5728833
## 34:       6    ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 35:       7                         ORF19 0.6046887 0.8596618 0.6312348
## 36:       7                         ORF52 0.6046887 0.8596618 0.6312348
## 37:       7                  ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 38:       7           ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 39:       8                         ORF24 0.9713771 0.9899227 0.9410908
## 40:       9           ORF27, ORF26, ORF25 0.9581874 0.9844445 0.9335398
## 41:       9                         ORF39 0.9581874 0.9844445 0.9335398
## 42:       9                  ORF45, ORF46 0.9581874 0.9844445 0.9335398
## 43:      10                  ORF53, ORF54 0.7865513 0.9466014 0.6044383
## 44:      11                       ORF64_1 0.9397368 0.9807196 0.8714120
## 45:      12                       ORF65_1 0.4822671 0.8939242 0.3442378
## 46:      12                ORF68, ORF67_1 0.4822671 0.8939242 0.3442378
## 47:      12                  ORF69, ORF70 0.4822671 0.8939242 0.3442378
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v           c       pchi
##           <num>        <num>       <num>      <num>       <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.000000000 0.00000000
##  6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
##  9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 25: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 26: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 27: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 35: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 36: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 37: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 38: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 39: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 40: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 41: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 42: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 43: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
## 44: 0.010922854 0.0043986223 0.003738478 -1.6009673 0.467876036 0.71047807
## 45: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 46: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 47: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
##           se.si        se.au       se.bp          v           c       pchi

## [1] "ORF3"                          "ORF74, ORF75, ORF76, ORF67 _2"
## [1] 2
##  [1] "ORF2"                          "ORF8"                         
##  [3] "ORF23"                         "ORF37, ORF36, ORF35, ORF35.5" 
##  [5] "ORF36"                         "ORF40"                        
##  [7] "ORF41, ORF42, OF43"            "ORF4"                         
##  [9] "ORF31"                         "ORF9"                         
## [11] "ORF10, ORF11"                  "ORF18"                        
## [13] "ORF22, ORF21, ORF20"           "ORF32, ORF33, ORF34"          
## [15] "ORF38"                         "ORF48, ORF49, ORF50, ORF51"   
## [17] "NOIR_1"                        "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2"                        "ORF19"                        
## [21] "ORF52"                         "ORF57, ORF58"                 
## [23] "ORF71, ORF72, ORF73"           "ORF53, ORF54"                 
## [25] "ORF65_1"                       "ORF68, ORF67_1"               
## [27] "ORF69, ORF70"
## [1] 27

Remove genes from clusters ?

##  [1] "ORF2"                          "ORF8"                         
##  [3] "ORF23"                         "ORF37, ORF36, ORF35, ORF35.5" 
##  [5] "ORF36"                         "ORF40"                        
##  [7] "ORF41, ORF42, OF43"            "ORF4"                         
##  [9] "ORF31"                         "ORF9"                         
## [11] "ORF10, ORF11"                  "ORF18"                        
## [13] "ORF22, ORF21, ORF20"           "ORF32, ORF33, ORF34"          
## [15] "ORF38"                         "ORF48, ORF49, ORF50, ORF51"   
## [17] "NOIR_1"                        "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2"                        "ORF19"                        
## [21] "ORF52"                         "ORF57, ORF58"                 
## [23] "ORF71, ORF72, ORF73"           "ORF53, ORF54"                 
## [25] "ORF65_1"                       "ORF68, ORF67_1"               
## [27] "ORF69, ORF70"
## [1] 27
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       5    10
##  2:       3     9
##  3:       2     7
##  4:       1     5
##  5:       7     4
##  6:       9     3
##  7:      12     3
##  8:       4     2
##  9:       6     1
## 10:       8     1
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters